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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-02-01, 16:24 CET based on data in: /hpc/uu_vet_iras/pliu/fastqc_report


        General Statistics

        Showing 360/360 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        DRR381601_1
        6.6%
        50%
        301 bp
        0.8
        DRR381601_2
        6.2%
        50%
        284 bp
        0.8
        DRR381603_1
        6.8%
        50%
        301 bp
        0.7
        DRR381603_2
        6.1%
        50%
        284 bp
        0.7
        DRR381607_1
        3.9%
        50%
        301 bp
        0.6
        DRR381607_2
        3.2%
        50%
        274 bp
        0.6
        DRR381616_1
        7.5%
        50%
        301 bp
        0.9
        DRR381616_2
        7.3%
        49%
        294 bp
        0.9
        DRR381634_1
        6.3%
        50%
        301 bp
        0.8
        DRR381634_2
        5.9%
        50%
        284 bp
        0.8
        DRR381635_1
        7.7%
        50%
        301 bp
        0.9
        DRR381635_2
        7.3%
        50%
        284 bp
        0.9
        DRR381661_1
        6.0%
        49%
        274 bp
        0.6
        DRR381661_2
        5.6%
        49%
        254 bp
        0.6
        DRR381665_1
        3.9%
        50%
        301 bp
        0.4
        DRR381665_2
        3.4%
        50%
        284 bp
        0.4
        DRR381669_1
        8.3%
        50%
        301 bp
        1.0
        DRR381669_2
        7.8%
        49%
        284 bp
        1.0
        DRR381701_1
        7.9%
        49%
        264 bp
        0.8
        DRR381701_2
        7.2%
        49%
        244 bp
        0.8
        DRR381723_1
        5.4%
        50%
        301 bp
        0.7
        DRR381723_2
        4.7%
        50%
        284 bp
        0.7
        DRR381735_1
        8.8%
        50%
        301 bp
        1.1
        DRR381735_2
        8.4%
        50%
        294 bp
        1.1
        DRR381740_1
        4.2%
        50%
        301 bp
        0.6
        DRR381740_2
        3.4%
        50%
        274 bp
        0.6
        DRR381743_1
        5.5%
        51%
        301 bp
        0.8
        DRR381743_2
        5.1%
        50%
        284 bp
        0.8
        DRR381744_1
        6.7%
        50%
        301 bp
        0.8
        DRR381744_2
        6.1%
        50%
        284 bp
        0.8
        DRR381745_1
        7.4%
        50%
        301 bp
        0.9
        DRR381745_2
        6.8%
        49%
        284 bp
        0.9
        DRR381749_1
        3.9%
        50%
        301 bp
        0.5
        DRR381749_2
        3.2%
        50%
        274 bp
        0.5
        SRR10119255_1
        20.0%
        50%
        217 bp
        1.1
        SRR10119255_2
        18.2%
        50%
        202 bp
        1.1
        SRR10119414_1
        24.1%
        50%
        192 bp
        1.4
        SRR10119414_2
        18.8%
        50%
        177 bp
        1.4
        SRR10337442_1
        19.9%
        50%
        247 bp
        0.8
        SRR10337442_2
        18.7%
        50%
        247 bp
        0.8
        SRR10506462_1
        16.6%
        51%
        251 bp
        0.8
        SRR10506462_2
        13.9%
        51%
        251 bp
        0.8
        SRR10520171_1
        27.0%
        50%
        151 bp
        1.8
        SRR10520171_2
        21.0%
        50%
        151 bp
        1.8
        SRR13160357_1
        14.5%
        50%
        251 bp
        0.7
        SRR13160357_2
        9.6%
        50%
        247 bp
        0.7
        SRR13160359_1
        20.3%
        50%
        251 bp
        1.0
        SRR13160359_2
        14.0%
        50%
        247 bp
        1.0
        SRR13160360_1
        14.0%
        50%
        251 bp
        0.7
        SRR13160360_2
        12.0%
        50%
        247 bp
        0.7
        SRR13167188_1
        19.0%
        50%
        251 bp
        0.8
        SRR13167188_2
        16.3%
        50%
        247 bp
        0.8
        SRR13498078_1
        63.8%
        50%
        34 bp
        0.9
        SRR13498078_2
        52.0%
        51%
        78 bp
        1.1
        SRR13498088_1
        66.8%
        52%
        34 bp
        1.0
        SRR13498088_2
        55.0%
        52%
        78 bp
        1.2
        SRR14419375_1
        20.1%
        51%
        301 bp
        0.9
        SRR14419375_2
        18.3%
        51%
        294 bp
        0.9
        SRR14419377_1
        21.8%
        51%
        294 bp
        0.9
        SRR14419377_2
        19.9%
        51%
        274 bp
        0.9
        SRR14419379_1
        15.5%
        51%
        294 bp
        0.6
        SRR14419379_2
        13.9%
        51%
        264 bp
        0.6
        SRR14419381_1
        20.1%
        51%
        301 bp
        0.7
        SRR14419381_2
        18.1%
        51%
        294 bp
        0.7
        SRR14419383_1
        18.0%
        51%
        301 bp
        0.7
        SRR14419383_2
        16.5%
        51%
        294 bp
        0.7
        SRR14419387_1
        17.6%
        51%
        294 bp
        0.8
        SRR14419387_2
        16.2%
        51%
        274 bp
        0.8
        SRR1509643_1
        13.5%
        50%
        251 bp
        3.0
        SRR1509643_2
        5.1%
        50%
        247 bp
        2.9
        SRR15277995_1
        4.0%
        50%
        254 bp
        0.6
        SRR15277995_2
        4.0%
        50%
        74 bp
        0.6
        SRR15277999_1
        4.6%
        50%
        234 bp
        0.6
        SRR15277999_2
        4.5%
        50%
        74 bp
        0.6
        SRR15376141_1
        4.5%
        50%
        301 bp
        0.8
        SRR15376141_2
        4.0%
        50%
        294 bp
        0.8
        SRR15376142_1
        4.7%
        50%
        301 bp
        0.8
        SRR15376142_2
        4.1%
        50%
        294 bp
        0.8
        SRR15376143_1
        5.1%
        50%
        301 bp
        0.9
        SRR15376143_2
        4.6%
        50%
        294 bp
        0.9
        SRR15376144_1
        18.6%
        51%
        294 bp
        0.8
        SRR15376144_2
        17.0%
        51%
        264 bp
        0.8
        SRR15376145_1
        18.3%
        51%
        301 bp
        0.8
        SRR15376145_2
        16.6%
        51%
        294 bp
        0.8
        SRR15376146_1
        16.4%
        51%
        301 bp
        0.7
        SRR15376146_2
        14.9%
        51%
        294 bp
        0.7
        SRR15376147_1
        19.2%
        51%
        294 bp
        0.8
        SRR15376147_2
        17.3%
        51%
        274 bp
        0.8
        SRR15376149_1
        21.0%
        51%
        294 bp
        0.8
        SRR15376149_2
        19.4%
        51%
        294 bp
        0.8
        SRR15376150_1
        18.6%
        51%
        294 bp
        0.8
        SRR15376150_2
        17.3%
        51%
        284 bp
        0.8
        SRR15376151_1
        16.1%
        51%
        301 bp
        0.7
        SRR15376151_2
        14.6%
        51%
        294 bp
        0.7
        SRR15376152_1
        19.3%
        51%
        294 bp
        0.9
        SRR15376152_2
        18.1%
        51%
        274 bp
        0.9
        SRR15376153_1
        16.7%
        51%
        301 bp
        0.7
        SRR15376153_2
        15.4%
        51%
        294 bp
        0.7
        SRR15376154_1
        19.9%
        51%
        294 bp
        0.9
        SRR15376154_2
        18.5%
        51%
        274 bp
        0.9
        SRR15415532_1
        17.8%
        51%
        294 bp
        0.8
        SRR15415532_2
        16.8%
        51%
        264 bp
        0.8
        SRR15415538_1
        21.5%
        51%
        274 bp
        0.9
        SRR15415538_2
        20.9%
        51%
        244 bp
        0.9
        SRR15415539_1
        22.1%
        51%
        284 bp
        1.1
        SRR15415539_2
        20.4%
        51%
        244 bp
        1.1
        SRR15415540_1
        19.4%
        52%
        264 bp
        0.8
        SRR15415540_2
        18.4%
        52%
        244 bp
        0.8
        SRR15415542_1
        16.2%
        51%
        294 bp
        0.6
        SRR15415542_2
        15.1%
        51%
        244 bp
        0.6
        SRR15415547_1
        14.4%
        51%
        284 bp
        0.5
        SRR15415547_2
        14.0%
        51%
        264 bp
        0.5
        SRR15415549_1
        16.0%
        51%
        254 bp
        0.7
        SRR15415549_2
        15.9%
        51%
        244 bp
        0.7
        SRR15415554_1
        20.4%
        51%
        264 bp
        1.0
        SRR15415554_2
        19.4%
        51%
        244 bp
        1.0
        SRR15415555_1
        18.5%
        51%
        294 bp
        0.8
        SRR15415555_2
        17.4%
        51%
        254 bp
        0.8
        SRR15415556_1
        23.2%
        52%
        274 bp
        1.0
        SRR15415556_2
        21.8%
        51%
        244 bp
        1.0
        SRR15415557_1
        16.0%
        51%
        274 bp
        0.7
        SRR15415557_2
        15.6%
        51%
        254 bp
        0.7
        SRR15415573_1
        13.9%
        51%
        274 bp
        0.5
        SRR15415573_2
        13.6%
        51%
        254 bp
        0.5
        SRR15415574_1
        18.4%
        52%
        284 bp
        0.8
        SRR15415574_2
        17.3%
        51%
        254 bp
        0.8
        SRR15415578_1
        17.1%
        51%
        294 bp
        0.8
        SRR15415578_2
        16.2%
        51%
        254 bp
        0.8
        SRR15415580_1
        4.8%
        50%
        251 bp
        0.9
        SRR15415580_2
        3.4%
        50%
        251 bp
        0.9
        SRR15415610_1
        13.6%
        51%
        274 bp
        0.6
        SRR15415610_2
        13.8%
        51%
        264 bp
        0.6
        SRR15415611_1
        20.3%
        51%
        274 bp
        1.0
        SRR15415611_2
        19.6%
        51%
        244 bp
        1.0
        SRR15415613_1
        8.4%
        50%
        294 bp
        1.7
        SRR15415613_2
        6.9%
        50%
        274 bp
        1.7
        SRR15415620_1
        15.1%
        51%
        254 bp
        0.7
        SRR15415620_2
        14.9%
        51%
        254 bp
        0.7
        SRR15415621_1
        19.3%
        51%
        244 bp
        0.9
        SRR15415621_2
        18.6%
        51%
        224 bp
        0.9
        SRR15415622_1
        13.1%
        51%
        294 bp
        0.6
        SRR15415622_2
        10.8%
        51%
        264 bp
        0.5
        SRR15415624_1
        27.4%
        51%
        294 bp
        1.6
        SRR15415624_2
        24.6%
        51%
        274 bp
        1.6
        SRR15674630_1
        33.1%
        50%
        151 bp
        1.2
        SRR15674630_2
        31.5%
        50%
        151 bp
        1.1
        SRR1714120_1
        18.4%
        50%
        251 bp
        0.8
        SRR1714120_2
        16.9%
        50%
        251 bp
        0.8
        SRR23929852_1
        28.3%
        50%
        247 bp
        1.3
        SRR23929852_2
        26.4%
        50%
        242 bp
        1.3
        SRR25510170_1
        18.5%
        50%
        251 bp
        0.6
        SRR25510170_2
        16.8%
        50%
        247 bp
        0.6
        SRR25523643_1
        23.3%
        50%
        251 bp
        1.0
        SRR25523643_2
        19.4%
        50%
        247 bp
        1.0
        SRR25523645_1
        19.8%
        50%
        251 bp
        0.7
        SRR25523645_2
        19.5%
        50%
        251 bp
        0.7
        SRR25551086_1
        15.9%
        50%
        251 bp
        0.5
        SRR25551086_2
        14.7%
        50%
        251 bp
        0.5
        SRR25603927_1
        17.1%
        50%
        251 bp
        0.7
        SRR25603927_2
        15.4%
        50%
        247 bp
        0.7
        SRR25603929_1
        15.5%
        50%
        251 bp
        0.6
        SRR25603929_2
        15.1%
        50%
        247 bp
        0.6
        SRR25603930_1
        16.8%
        50%
        251 bp
        0.7
        SRR25603930_2
        16.8%
        50%
        247 bp
        0.7
        SRR2762258_1
        8.8%
        51%
        247 bp
        0.3
        SRR2762258_2
        7.9%
        51%
        247 bp
        0.3
        SRR2914453_1
        13.1%
        50%
        247 bp
        0.5
        SRR2914453_2
        11.4%
        50%
        247 bp
        0.5
        SRR2914455_1
        19.4%
        49%
        247 bp
        0.7
        SRR2914455_2
        18.0%
        49%
        247 bp
        0.7
        SRR3180501_1
        11.8%
        48%
        251 bp
        1.7
        SRR3180501_2
        10.9%
        48%
        247 bp
        1.7
        SRR3180502_1
        11.7%
        48%
        251 bp
        1.9
        SRR3180502_2
        10.4%
        48%
        247 bp
        1.8
        SRR3180707_1
        9.5%
        50%
        251 bp
        1.6
        SRR3180707_2
        8.5%
        50%
        247 bp
        1.6
        SRR3191403_1
        16.9%
        49%
        247 bp
        0.6
        SRR3191403_2
        15.3%
        49%
        247 bp
        0.6
        SRR3195765_1
        20.0%
        51%
        284 bp
        0.9
        SRR3195765_2
        17.2%
        51%
        234 bp
        0.9
        SRR3195836_1
        19.5%
        51%
        264 bp
        0.9
        SRR3195836_2
        17.5%
        51%
        214 bp
        0.9
        SRR3195839_1
        11.5%
        51%
        294 bp
        0.4
        SRR3195839_2
        8.3%
        51%
        224 bp
        0.4
        SRR3195840_1
        17.4%
        51%
        294 bp
        0.8
        SRR3195840_2
        14.9%
        51%
        234 bp
        0.8
        SRR3195841_1
        20.0%
        51%
        284 bp
        0.8
        SRR3195841_2
        17.6%
        51%
        224 bp
        0.8
        SRR3195851_1
        12.1%
        51%
        294 bp
        0.4
        SRR3195851_2
        9.4%
        51%
        224 bp
        0.4
        SRR3195852_1
        14.4%
        51%
        294 bp
        0.5
        SRR3195852_2
        11.5%
        51%
        224 bp
        0.5
        SRR3205742_1
        8.5%
        49%
        251 bp
        1.4
        SRR3205742_2
        8.2%
        49%
        247 bp
        1.4
        SRR3205757_1
        7.4%
        50%
        251 bp
        1.1
        SRR3205757_2
        6.9%
        50%
        251 bp
        1.1
        SRR3224568_1
        10.2%
        50%
        251 bp
        1.7
        SRR3224568_2
        9.6%
        50%
        247 bp
        1.7
        SRR3224814_1
        12.9%
        49%
        251 bp
        1.9
        SRR3224814_2
        11.8%
        49%
        251 bp
        1.9
        SRR4301494_1
        9.1%
        50%
        254 bp
        0.4
        SRR4301494_2
        8.7%
        50%
        214 bp
        0.4
        SRR4301497_1
        13.5%
        50%
        284 bp
        0.6
        SRR4301497_2
        11.5%
        50%
        254 bp
        0.5
        SRR4301501_1
        10.1%
        51%
        294 bp
        0.4
        SRR4301501_2
        6.2%
        51%
        234 bp
        0.4
        SRR4301505_1
        8.6%
        51%
        294 bp
        0.3
        SRR4301505_2
        5.9%
        51%
        244 bp
        0.3
        SRR4301513_1
        14.9%
        51%
        294 bp
        0.5
        SRR4301513_2
        12.3%
        51%
        244 bp
        0.5
        SRR4301514_1
        14.0%
        51%
        294 bp
        0.6
        SRR4301514_2
        10.5%
        51%
        244 bp
        0.6
        SRR4301519_1
        14.5%
        50%
        274 bp
        0.7
        SRR4301519_2
        11.8%
        50%
        234 bp
        0.7
        SRR4301521_1
        14.6%
        50%
        274 bp
        0.6
        SRR4301521_2
        11.5%
        50%
        234 bp
        0.6
        SRR4301522_1
        15.4%
        51%
        294 bp
        0.6
        SRR4301522_2
        11.8%
        50%
        244 bp
        0.6
        SRR4301525_1
        13.4%
        51%
        294 bp
        0.5
        SRR4301525_2
        11.6%
        51%
        254 bp
        0.5
        SRR4301527_1
        15.5%
        51%
        284 bp
        0.6
        SRR4301527_2
        12.5%
        51%
        244 bp
        0.6
        SRR4301531_1
        15.4%
        51%
        294 bp
        0.6
        SRR4301531_2
        13.1%
        51%
        274 bp
        0.6
        SRR4301544_1
        13.6%
        51%
        294 bp
        0.5
        SRR4301544_2
        12.2%
        51%
        284 bp
        0.5
        SRR4301548_1
        11.8%
        51%
        294 bp
        0.5
        SRR4301548_2
        9.6%
        51%
        254 bp
        0.5
        SRR4301550_1
        14.0%
        51%
        294 bp
        0.5
        SRR4301550_2
        10.8%
        51%
        264 bp
        0.5
        SRR4301554_1
        15.1%
        51%
        294 bp
        0.6
        SRR4301554_2
        12.9%
        51%
        284 bp
        0.6
        SRR4301555_1
        17.0%
        51%
        294 bp
        0.7
        SRR4301555_2
        14.6%
        51%
        274 bp
        0.7
        SRR4301562_1
        19.0%
        51%
        284 bp
        0.8
        SRR4301562_2
        17.0%
        51%
        254 bp
        0.8
        SRR4301564_1
        16.2%
        51%
        294 bp
        0.7
        SRR4301564_2
        14.1%
        51%
        274 bp
        0.7
        SRR4301569_1
        16.3%
        50%
        294 bp
        0.7
        SRR4301569_2
        14.4%
        50%
        264 bp
        0.7
        SRR4301571_1
        15.6%
        50%
        294 bp
        0.6
        SRR4301571_2
        13.4%
        50%
        264 bp
        0.6
        SRR4301574_1
        18.6%
        51%
        294 bp
        0.8
        SRR4301574_2
        17.5%
        51%
        264 bp
        0.8
        SRR4301577_1
        17.8%
        51%
        294 bp
        0.7
        SRR4301577_2
        16.4%
        51%
        264 bp
        0.7
        SRR4301579_1
        17.5%
        51%
        294 bp
        0.7
        SRR4301579_2
        15.8%
        51%
        264 bp
        0.7
        SRR4301588_1
        26.4%
        51%
        244 bp
        1.4
        SRR4301588_2
        25.6%
        51%
        224 bp
        1.4
        SRR5413253_1
        42.7%
        49%
        151 bp
        10.6
        SRR5413253_2
        38.5%
        49%
        151 bp
        10.6
        SRR5864678_1
        13.4%
        50%
        247 bp
        0.6
        SRR5864678_2
        12.8%
        50%
        232 bp
        0.6
        SRR5870510_1
        20.8%
        50%
        247 bp
        1.0
        SRR5870510_2
        18.7%
        50%
        232 bp
        1.0
        SRR6118141_1
        7.1%
        50%
        247 bp
        1.3
        SRR6118141_2
        6.4%
        50%
        242 bp
        1.3
        SRR6118142_1
        3.9%
        50%
        247 bp
        0.7
        SRR6118142_2
        3.3%
        50%
        242 bp
        0.7
        SRR6373397_1
        35.0%
        51%
        251 bp
        2.3
        SRR6373397_2
        32.9%
        51%
        251 bp
        2.3
        SRR6929601_1
        17.0%
        51%
        301 bp
        0.7
        SRR6929601_2
        15.6%
        51%
        284 bp
        0.7
        SRR6929602_1
        17.2%
        51%
        301 bp
        0.7
        SRR6929602_2
        15.3%
        51%
        294 bp
        0.7
        SRR6929603_1
        20.3%
        51%
        254 bp
        0.9
        SRR6929603_2
        18.4%
        51%
        214 bp
        0.9
        SRR6929604_1
        20.1%
        51%
        274 bp
        0.9
        SRR6929604_2
        17.6%
        51%
        224 bp
        0.9
        SRR6929605_1
        22.5%
        51%
        274 bp
        1.1
        SRR6929605_2
        19.3%
        51%
        224 bp
        1.1
        SRR6929606_1
        20.3%
        51%
        284 bp
        0.9
        SRR6929606_2
        17.5%
        51%
        224 bp
        0.9
        SRR6929607_1
        25.7%
        51%
        284 bp
        1.3
        SRR6929607_2
        20.0%
        51%
        214 bp
        1.3
        SRR6929608_1
        25.2%
        51%
        264 bp
        1.3
        SRR6929608_2
        21.2%
        51%
        214 bp
        1.3
        SRR6929609_1
        20.0%
        51%
        284 bp
        0.9
        SRR6929609_2
        17.2%
        51%
        234 bp
        0.9
        SRR6929610_1
        15.1%
        51%
        294 bp
        0.6
        SRR6929610_2
        12.0%
        51%
        234 bp
        0.6
        SRR6929611_1
        5.5%
        50%
        254 bp
        1.1
        SRR6929611_2
        4.1%
        50%
        254 bp
        1.1
        SRR6929612_1
        6.1%
        50%
        294 bp
        1.1
        SRR6929612_2
        5.2%
        50%
        284 bp
        1.1
        SRR6929613_1
        7.9%
        50%
        294 bp
        1.5
        SRR6929613_2
        6.6%
        50%
        294 bp
        1.5
        SRR6929614_1
        2.8%
        50%
        251 bp
        0.5
        SRR6929614_2
        2.0%
        50%
        251 bp
        0.5
        SRR6929615_1
        3.2%
        50%
        251 bp
        0.6
        SRR6929615_2
        2.5%
        50%
        251 bp
        0.6
        SRR6929616_1
        7.5%
        50%
        301 bp
        1.5
        SRR6929616_2
        5.8%
        50%
        294 bp
        1.5
        SRR6929617_1
        11.2%
        50%
        301 bp
        2.3
        SRR6929617_2
        8.9%
        50%
        294 bp
        2.3
        SRR6929618_1
        8.1%
        50%
        301 bp
        1.6
        SRR6929618_2
        6.4%
        50%
        294 bp
        1.6
        SRR6929619_1
        9.6%
        50%
        301 bp
        2.0
        SRR6929619_2
        7.5%
        50%
        294 bp
        2.0
        SRR6929620_1
        6.5%
        50%
        294 bp
        1.2
        SRR6929620_2
        5.6%
        50%
        294 bp
        1.2
        SRR6929621_1
        7.2%
        50%
        294 bp
        1.3
        SRR6929621_2
        6.2%
        50%
        284 bp
        1.3
        SRR6929622_1
        7.8%
        50%
        244 bp
        1.6
        SRR6929622_2
        6.7%
        50%
        284 bp
        1.6
        SRR6929623_1
        5.3%
        50%
        301 bp
        1.1
        SRR6929623_2
        4.6%
        51%
        301 bp
        1.1
        SRR6929624_1
        20.2%
        51%
        294 bp
        0.9
        SRR6929624_2
        17.9%
        51%
        264 bp
        0.9
        SRR6929625_1
        16.5%
        51%
        294 bp
        0.7
        SRR6929625_2
        14.9%
        51%
        274 bp
        0.7
        SRR6929626_1
        17.6%
        51%
        294 bp
        0.8
        SRR6929626_2
        15.2%
        51%
        274 bp
        0.8
        SRR6929627_1
        21.7%
        51%
        294 bp
        1.0
        SRR6929627_2
        20.0%
        51%
        264 bp
        1.0
        SRR6929628_1
        17.4%
        51%
        301 bp
        0.8
        SRR6929628_2
        15.4%
        51%
        294 bp
        0.8
        SRR6929629_1
        17.7%
        51%
        301 bp
        0.8
        SRR6929629_2
        16.2%
        51%
        284 bp
        0.8
        SRR6929630_1
        17.6%
        51%
        301 bp
        0.8
        SRR6929630_2
        15.4%
        51%
        294 bp
        0.8
        SRR6929631_1
        19.7%
        51%
        301 bp
        0.9
        SRR6929631_2
        17.8%
        51%
        294 bp
        0.9
        SRR6929632_1
        4.2%
        50%
        244 bp
        0.8
        SRR6929632_2
        3.4%
        50%
        274 bp
        0.8
        SRR6929633_1
        4.3%
        50%
        244 bp
        0.8
        SRR6929633_2
        3.4%
        50%
        274 bp
        0.8
        SRR6929634_1
        4.1%
        50%
        244 bp
        0.8
        SRR6929634_2
        3.4%
        50%
        274 bp
        0.8
        SRR6929635_1
        4.9%
        50%
        254 bp
        0.9
        SRR6929635_2
        4.3%
        50%
        284 bp
        0.9
        SRR6929636_1
        19.5%
        51%
        294 bp
        0.9
        SRR6929636_2
        16.8%
        51%
        274 bp
        0.9
        SRR6929637_1
        20.6%
        51%
        294 bp
        0.9
        SRR6929637_2
        18.1%
        51%
        274 bp
        0.9
        SRR6929638_1
        9.9%
        50%
        294 bp
        2.0
        SRR6929638_2
        8.1%
        50%
        284 bp
        2.0
        SRR6929639_1
        11.5%
        50%
        294 bp
        2.3
        SRR6929639_2
        9.8%
        50%
        294 bp
        2.2
        SRR7439153_1
        15.7%
        50%
        247 bp
        0.7
        SRR7439153_2
        14.3%
        50%
        247 bp
        0.7
        SRR7460819_1
        11.0%
        51%
        251 bp
        0.4
        SRR7460819_2
        9.3%
        51%
        247 bp
        0.4
        SRR7896257_1
        8.9%
        49%
        244 bp
        1.5
        SRR7896257_2
        7.7%
        49%
        204 bp
        1.4
        SRR8192791_1
        24.7%
        50%
        202 bp
        1.5
        SRR8192791_2
        23.3%
        51%
        197 bp
        1.5
        SRR8292155_1
        5.4%
        50%
        251 bp
        1.0
        SRR8292155_2
        4.5%
        50%
        217 bp
        1.0
        SRR941218_1
        39.0%
        50%
        146 bp
        2.2
        SRR941218_2
        37.0%
        50%
        146 bp
        2.2
        SRR9694420_1
        45.5%
        51%
        247 bp
        3.5
        SRR9694420_2
        42.9%
        51%
        242 bp
        3.5
        SRR9994124_1
        7.0%
        50%
        247 bp
        1.3
        SRR9994124_2
        6.2%
        50%
        247 bp
        1.3
        SRR9994125_1
        7.5%
        50%
        247 bp
        1.4
        SRR9994125_2
        6.7%
        50%
        242 bp
        1.4
        SRR9994127_1
        6.3%
        50%
        247 bp
        1.1
        SRR9994127_2
        5.6%
        50%
        242 bp
        1.1

        FastQC

        Version: 0.12.1

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        GGTTAAGCGACTAAGCGTACACGGTGGATG
        2
        21788
        0.0061%
        CCTTAAAGAAGCGTACTTTGCAGTGCTCACACA
        2
        20426
        0.0057%
        AAATTGAAGAGTTTGATCATGGCTCAGATTGAACG
        2
        37963
        0.0107%
        CCTTAAAGAACTGTACTTTGCAGTGCTCACACA
        2
        13081
        0.0037%
        AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCT
        2
        28540
        0.0080%
        AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTA
        2
        15284
        0.0043%
        GGTTAAGCGACTAAGCGTACACGGTGGATGC
        2
        8129
        0.0023%
        AAATTGAAGAGTTTGATCATGGCTCAGATTGAAC
        2
        17562
        0.0049%
        AAATTGAAGAGTTTGATC
        2
        12016
        0.0034%
        GCGAAGGTGGCGGAATTGG
        2
        8965
        0.0025%
        AAATTGAAGAGTTTGATCATGGCTCAGATT
        2
        12055
        0.0034%
        AAATTGAAGAGTTTGATCATGGCT
        2
        7017
        0.0020%
        TGCCTGGCGGCCTTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCA
        2
        3712
        0.0010%
        GGTTAAGCGACTAAGCGTACACGGTGGAT
        2
        4136
        0.0012%
        ATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTT
        2
        3519
        0.0010%
        TGTCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCA
        2
        4566
        0.0013%
        GAGGTACTGCAGACGACTCGC
        2
        3326
        0.0009%
        AAATTGAAGAGTTTGATCATG
        2
        4937
        0.0014%
        AAATTGAAGAGTTTGATCATGGCTCAGA
        2
        5072
        0.0014%
        AGGTACTGCAGACGACTCGC
        2
        3520
        0.0010%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        loading..

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1